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Thursday, October 5, 2017

Upper Paleolithic genomes from Sunghir, Russia (Sikora et al. 2017)

Over at Science at this LINK. Not surprisingly, these four Sunghir individuals are very similar to another Upper Paleolithic Eastern European, Kostenki14, in terms of both genome-wide genetic structure and uniparental markers (Y-haplogroup C1a2, mtDNA-haplogroups U2 and U8c). If you can't access the paper, the supplementary materials are freely available here, and there's a press release here.

Abstract: Present-day hunter-gatherers (HGs) live in multilevel social groups essential to sustain a population structure characterized by limited levels of within-band relatedness and inbreeding. When these wider social networks evolved among HGs is unknown. Here, we investigate whether the contemporary HG strategy was already present in the Upper Paleolithic (UP), using complete genome sequences from Sunghir, a site dated to ~34 thousand years BP (kya) containing multiple anatomically modern human (AMH) individuals. We demonstrate that individuals at Sunghir derive from a population of small effective size, with limited kinship and levels of inbreeding similar to HG populations. Our findings suggest that UP social organization was similar to that of living HGs, with limited relatedness within residential groups embedded in a larger mating network.

@epoch2013, if you go by the model Ancient North Eurasians being Sunghir+ENA (which seems worth testing eventually in qpGraph, though seems hard to know how anyone can know without testing), then it may not be a single small population and it may just be than all these populations are varying independent mixes of the Basal_Eurasian+Villabruna+Sunghir+ENA ancestries. I am not sure about this though.

It'll be shown by dropping the Sunghir samples into a qpGraph, or it won't. (Question is whether these specific people are right, not whether some UP Euro related group divergent from the samples in Fu et al is!) Not much room to debate around it before anyone does that.

@MaxT:C1 Y-DNA again!? amazing to see how wide spread it was once.

Though these y chromosomes are not necessarily closer to those individuals today who are in present day C1 groupings, than R is to G...

Very distant branches whose whole lower branching tree has left no descendants today...

http://3.bp.blogspot.com/-5cWLu_X84is/VQRecy3MHyI/AAAAAAAAJ_0/8fnpuYYQ_4Q/s1600/figure1.jpg - in our history, the GT tree left lots of descendants all over Eurasia from East to West, while the C tree has left very few, only in the Eastern fringes of Eurasia. (I would say only due to luck, but who knows?).

(Sunghir population seems to had a tiny population size also, compared to Ust Ishim, who himself is the representative of an extinct lineage, albeit, as a fairly derived node on the GT tree closer to the people who did leave widespread descendants today).

Not relevant to the topic at hand, but every time I see a science paper with unnecessary abbreviations (HG, UP), I want to kick a puppy. It makes reading the papers more difficult, and I can't imagine that the characters saved are being donated to illiterate children in the Third World. Unless you've got a good reason - deoxyribonucleic acid - write it out.

Chad, this is not so, you write something that contradicts the text. ANE is not a mixture, or rather, no mixes do not exist, all components are mixtures. Guys of Sunghir is not ANE. They like Kostenki extincted.

@Epoch - Keep in mind that the areas that likely had larger population sizes are also much harder to get samples from. We may be seeing a biased picture here. In fact, a lot of the best sites are probably under a few hundred feet of water.

"The third individual in Burial 2 (SIV) was represented only by the diaphysis (midsection)of a human femur, which had been polished, hollowed-out and filled with ochre, andcarefully placed next to SII. That it is a single element (and not an entire skeleton), and evidence from its bone chemistry which indicates “a different geographic origin for that individual and/or a contrasting post-mortem history,” suggests that the SIV femur section might have been an heirloom piece from an individual who died earlier than SII and SIII. Regardless, that individual presumably had not died significantly earlier than SII and SIII, since his remains were still available to them to collect. Hence, it is of similar age, perhaps someone who had died relatively recently or within generational memory of the individuals in the double burial"

He probably died out on a trek or hunt somewhere, and was brought back for burial. Or at least a piece of his leg was.

They do an extensive paper, full of info and then put .jpg minuscule graphs inside, instead of vectors, which means that when you zoom you can't see anything.No Bayesians as well. Is Reichlab that much better in formating their work?

I'm not sure what else "ANE is these guys plus ENA" could mean other than a special relationship between the Sunghir samples and ANE? At least we've got it cleared up.

@MaxT, right, as you noted, no sign of any enriched sharing with Sunghir and ANE derived (MA1, AG3, EHG) in any of their measures in the Supplement.

Not Fig. S26, not Fig. S19, not Fig. S18, not nuthin'.

The qpGraph do show that Sunghir, Vestonice, Kostenki, GoyetQ116-1 are all effectively a clade to MA-1 (none is more related and they all diverge from a population which had split from MA-1's ancestor).

Though as Chad would probably note, they do show a worst Z stat for relatedness between Villabruna and MA-1, which is likely mediated through ancestry from a population related to ENA.

You're cherry picking one comment over another. ANE is UP Euro-related plus ENA. Neither of these UP will be much closer to MA1 without ENA. They're not differentiated enough for any real significance.

If you want more specifics, the difference in drift between the samples and anyone else is quite small. They are not very differentiated. However, if you go f4 (Onge, MA1; UP_Euro, UP Euro), there is no real difference between Kostenki and Vestonice. However, both are about significantly better than Goyet as the admixing source. The trees do the same thing. A branch from by Vestonice and Kostenki are the admixing source for ANE. Also, drift lengths between these samples is very tiny when you put them on the same tree.

Sunghir (& Kostenki) treat Vestonice cluster (Y C1a2, mt U8c) which has no modern descendants. Essentially, these people almost did not participate in the formation of modern populations or their participation was minimal, through mt U2.

How can we say that a certain population did not contribute or participate in the formation of modern populations when we see Neanderthal contributed without leaving any sign of their Y-DNA or MtDNA Haplogroups ?

Rather, they are primarily descended from a stream of populations which constituted a "sister clade" to "West Eurasian" (basically, "North Eurasians proper"), but with additional ENA admixture.

These Sunghir genomes seem to be West Eurasians without ENA admixture, not North Eurasians without ENA admixture.

(We can't apply the modern conceptualization of West Eurasia to these ancient populations, since modern West Eurasians are a complex mix of ancient West Eurasian, North Eurasian, ENA, Basal Eurasian, and African ancestries)

WHG also has the relationship with farmers, not in MA1 or UP Euros. That is, I think, where the difference is. The difference between Kostenki and Vestonice from what is in MA1 seems very minimal if there is any at all. I don't like ghosts. One can simply materialize one anywhere on a graph for many things. It doesn't mean it's real.

Anyway, plug in the programs and try this yourselves. You will not get a West Eurasian source into MA1 without branching between Kostenki and Vestonice, or branching off from pre-Vestonice, after breaking with Kostenki. It's the only way to keep the Z below 3.

@Chad: An effective almost trifurcation between the UP Euro related parts of MA-1, Kostenki-Sunghir and GoyetQ116-Villabruna with MA-1 shallowly on the K-S side seems very possible compared to the Lipson model of MA-1 basal to the other UP Euros that Sein relates.

The drift lengths (e.g. simple outgroup f3 statistics) just don't seem to fit with MA-1's West Eurasian ancestry drifting with the Sunghir-Kostenki subgroup for any substantial length of time.

I did want to say though about: "Also, drift lengths between these samples is very tiny when you put them on the same tree", this paper's supplement S10 notes:

"Sunghir / Kostenki 14 - We find that SIII shows substantial population-specific drift with all tested individuals, except the other individuals from the same site. The lowest estimates outside Sunghir are obtained with Kostenki 14, consistent with results from the ancestry analyses. However, despite their affinity, the results also show substantial amounts of drift specific to Kostenki 14 after its divergence, therefore rejecting a directly ancestral relationship to Sunghir. Estimates are high for both Sunghir and Kostenki 14 when compared to later European HGs, suggesting that despite their shared early European ancestry, they did not form a direct ancestral group to the later European HGs in our dataset."

"WHG also has the relationship with farmers, not in MA1 or UP Euros. That is, I think, where the difference is. The difference between Kostenki and Vestonice from what is in MA1 seems very minimal if there is any at all. I don't like ghosts. One can simply materialize one anywhere on a graph for many things. It doesn't mean it's real."

But for this case (farmer relation) the ghost may be real. I read that Ofer Bar-Yosef considers the Levantine Aurignac to be very real, to have a very real connection to very early West-European Aurignac. If you take a look at the D-stats in Fu et al that paper uses Iraqi-Jew. If you do the same D-stats but swap Iraqi-Jew for Anatolina, Natufian, Iran_NL and Iran_CHL you'll find that Anatolian and Natufian show similar affinity to WHG as Iraqi_jew, Iran_NL shows nothing and Iran_Chl show some.

Couldn't there have been a ghost population in Europe around the LGM, apart from the usual suspects, with roots in the Aurignac but different from Goyet/Magdalenian? Something must link WHG to Natufians without Natufians coming to Europe because there is no Basal in WHG.

''Sunghir 3 clusters with an individual from Nepal (nep-0172; 96/100replicates) carrying the C1a2-defining V20 mutation, albeit with an early divergence close to the split with haplogroup C1a1 (represented by individual JPT-NA18974 from Japan) (Fig. S8). The deep divergences and widespread geographical distribution observed in the descendants of these haplogroups suggest a rapid dispersal of these lineages during the Upper Palaeolithic.''

R1b and I2a come from completely different sources. I2a is a local pan-European haplogroup leaving the roots in the West Asia, R1b it came in epipaleolithic from Siberia or the Urals. The fact that they were distributed in the Epigravettianculture, it does not say that they further spread from Italy or from SEE. The eastern Epigravettian culture was widespread in the Northern Black Sea region also, where we see R1b and I2a in the Mesolithic and Neolithic.

Rob, you are wrong. Y-hg IJ > I has roots in the West Asian. Siberian Mal'ta 24000 BP is R*, I & I2a is in hole Europe, J is the West Asian. European Paleolithic mtDNA extincted.

Your reasoning is that R1b spread from Italy and SEE nothing at unreasonable, it's just nobody knows. Your reasoning about R1b and I2a somehow related by descent or distribution at all unjustified. You contradict all the studies. I wrote to you that the spread of I2a has nothing to do with the spread of R1b, they have completely different sources & routs & times of spread and of fates.

I agree. Some idiots try and lump Haplogroup I in with R, when they are completely different. It's the same bs with people who lump haplogroups G,J, E and T together with all being of them being "Neolithic". Just not a fact.

No duh, sherlock. But that´s not what you said, you said I2a is ´leaving its roots in West Asia´, whatever that means. So youre inaccurate, I2a had long been in Europe when it expanded.

" Siberian Mal'ta 24000 BP is R*, I & I2a is in hole Europe, J is the West Asian."'You are talking about MUP. i am talking about the LUP -glacial expansions.Different epochs, go look it up.And I2a was NOT in ´hole´(i gather you mean whole) of Europ, because the Aurignacians and Magdalenians are not I2a, not even the Dolni Vestonice Gravettians were.

-"Your reasoning about R1b and I2a somehow related by descent or distribution at all unjustified" no its not unjustified, you just cant grasp the details. For a start, i never suggested that R1b and I2a are phylogenetically related, I do know how the alphabet goesRather, i suggested that present evidence points to L751 and I2-L460 closely correlating with WHG/ UHG / and WHG-containing late glacial -mesolithic groups. To repeat, this does not mean I am saying R1b originated in SEE or Europe, nor that they exactly correspond.

@Richard

"Some idiots try and lump Haplogroup I in with R"If you weren´t an ignorant snowflake cry-baby, you´d gather what i meant.

The 95% confidence intervals of YFull's TMRCA estimates do not provide any reliable evidence that might allow one to reject a hypothesis of a simultaneous origin Y-DNA haplogroups C1a2 and I, perhaps concomitant with the entry into Europe of AMHs and the appearance in that region of Upper Paleolithic industry.

The coalescence age of I2 and the coalescence age of C1a2a (extant European C1a2 plus a basal branch found in an ethnic Armenian) are significantly younger still, and not significantly different from each other:

The Y-DNA ancestry of the tested La Braña specimen seems to have diverged from that of extant European & Armenian members of C1a2a during the course of C1a2's expansion into Europe with Upper Paleolithic industry. I would like to see the Y-DNA of the Sunghir specimens, the Nepalese individual (nep-0172) mentioned in the passage quoted by Nirjhar, and a rumored Algerian member of C1a2 added to YFull's tree to see where they fit in vis-à-vis La Braña.

@Rob, you wrote "So R1b expanded from SEE....and Italy" that it is not fact. This unfounded statement in any case.

You wrote "looking at it R1b- L754 & I2a-L46o do seem to correlate with proto-Villabruna at a GW level; and they can have only expanded from SEE" that it is not fact. This unjustified statement in any case.

Where is the earliest eivdence of UHG / prot-VB admxiture ? - Dolni Vestonice in ECE, none in western Europe Aurignacian (Goyet), none in EE plain (SUnghir, Kostenki´s). Where is the next earliest evidence of its presence - El Miron & VB.

And my point was that L754 lineages seem to have diversified around s o e Europe, which they clealry did.

"and from the East Eurasian side of ANE'sheritage."

I think it's more Complex than that Villabruna, Blatterhohle (pre-M269 WHG -EEF hybrid) dont have any ANE The R1b in iron gates and Latvia have minimal EHG/ ANE.So what evidence is your statement based on ?

The latest Mathieson paper did model Latvian HG as partially EHG. The Ukranian HG were also similar to EHG and R1b, rather than WHG. I suspect that the meeting point between WHG and EHG was extremely early, such that some early branches of R1b, like the NE Italian "Villabrunan" looked exactly like their western I2 counterparts genetically over a few thousand years.

Recall that even some I2, and C-V20 that appear in the European Neolithic look almost identical to their EEF counterparts, a process of admixture over a few centuries. It must have really depended on the tribe, and which HG groups were absorbed while others remained isolated and died out.

I would be bit more nuanced about R1b being a WHG marker, I think it's more safe to say that some subsets of R1b may be connected with WHG. The ''ancestral'' subset of R1b could be still of EHG origin. All in all, R1s seem to be likely interconnected.

- "The Ukranian HG were also similar to EHG and R1b, rather than WHG."Curiously these Ukrainian Mesolithcis that are shifted toward EHG are virtually all I2a2. When R1b starts appearing in Neolithic, there is a slight WHG shift.

Also, we have blatterhohlewhich is basically WHG / EEF, with no ANE.

And again, there are samples from Mesolithic & EN Siberia. Are you aware of the absence of R1b of any sort ?

Just remember that I2a dominated the earlier European samples and very few untill recently expected R1b to be anywhere near the Balkans during the Mesolithic....There is still a huge area between Southern Siberia and the Balkans. R1b might surprise us again...

NO I agree that Siberia isn.t synonymous with ANE, and to clarify again, its abundantly clear that R1b is ultimately eastern. So if you're suggesting the Urals ad Siberia, - where exactly ? Is there any clear evidence for a uralian refuge ? I know there are some cave´type sites in the Urals, which might vae been visited during the LGM, but anything else ?

@ Ric

"Just remember that I2a dominated the earlier European samples and very few untill recently expected R1b to be anywhere near the Balkans during the Mesolithic"

"south of eastern Europe" is not equal your SEE=SouthEastern Europe, see https://en.wikipedia.org/wiki/Southeast_Europe , Northern Black Sea region is not its par"

Which is why I clarified abundatly "sensu latu" - as in the wide meaning, also taken by the recent Mathieson paper. The Black Sea littoral & adjacent Anatolia, the northern Balkans etc. This was a unit during the LGM. Obviously I am not referring to Crete or Peloponessus.

Also I'd suggest taking a look at the qpAdm runs in Mathieson that compare autosomal DNA to X chromosomes. They have the increase of EHG in the Middle Neolithic coming entirely from male WHG. Admixture of 16% male WHG and 0% female WHG. Pretty stark contrast there.

Doing a similar analysis with Bell Beakers as a mixture of CWC + the Neolithic population that fits best (or maybe Neolithic + WHG) could tell us for sure to what extent Bell Beakers received their steppe ancestry for men and to what extent it came from women.

http://www.nature.com/articles/srep44585?WT.feed_name=subjects_evolution for mammoths

The Asian mammoth mitochondrial DNA clade which seemingly back-migrated from America (hg DE) is estimated to have split from American sister branch close to 500 000 years ago, and the Eurasian DE clade (which contains some European specimens) looks to be around 200 000 years old.

According to the 2008 paper Siberia went from being dominated by haplogroup A before 44 000 years ago to being all DE afterward (but DE was already present as a minority earlier). But there was only one European sample in that one. In the new paper there are a bunch of European samples; it seems that some DE showed up but Europe was still predominantly B2 in the Upper Palaeolithic.

This is all mitochondrial DNA though. Obviously they need to step up their game and get into full genomes.

So anyway in a nutshell probably mammoth herds moving from eastern Siberia toward Europe yes, but from America in the time frame you are thinking of no.

Yes, it is interesting that C1a survived in the 'peripheries' of Europe - Iberia & Anatolia, with its offshoots in EN Bulgaria & Cardial Dalmatia, eg. As you said, the modern Europeans who are C1a are derived from the Anatolian branch rather than La Brana, and the 2 diverged as much as 43 ky ago.

I know Reich & Lipson accounted for ENA. Fu et al didn't. Again, you are not paying attention. Also, no where in Reich & Lipson do they say pre-K14. It is a sister branch. Which works well as a split from Vestonice. Once again, you refuse to look at anything I type. If you aren't going to actually read what I actually type, I will not respond to you.

You did not use ANE in this run. Karitiana who score 45% ANE (in Basal-rich K7 cal), we see majority of their ANE was disappearing into ENA in your graph, Karitiana end up being 83% ENA and rest 17% K14 (instead of 45% ANE+ 55% ENA). K17 itself appears to have 23% ENA on your qpAdm.

Based on qpAdm score, i can see that it was a successful test. We see a pattern where ENA ancestry exists in both groups. Again pointing to some ghost population, older, less divergent than K14.

You're off-base. Just trust what I am telling you. It isn't older, but a sister clade. Fig 4 is the same thing. You're not understanding at all! It doesn't branch off before Kostenki's line, but at it. Forget some old qpAdm. I have no time to argue this with you. If you want to see a tree, go to Anthrogenica on this subject. I posted one and will put up several others tomorrow if I have time.

Right..... It's not an older branch, but a sister branch. Think of it as a tuning fork. One side doesn't come off before the other. I don't know how much easier I can try to explain this for you. The West Eurasian side of MA1 wouldn't be a little closer to Vestonice than Kostenki if it were diverged earlier than Kostenki. You would be getting into the Ust_Ishim time-frame. But, believe whatever you wish.

Vestonice cluster (Vestonice, Kostenki, Ostuni) WHG belongs to East Gravettian culture aka Kostenki-Willendorf culture. It has not ANE and was not involved in the formation of ANE.Villabruna cluster WHG belongs to Epigravettian culture (& to other final paleolithic cultures). It has ANE-like participants (EHG?).Epigravettian means "after gravettian", it did not come directly from the Gravette.

I might be mistaken but I don't think these D-stats mean Villabruna doesn't like Vestonice, it means Villabruna shares considerably more drift with EHG than Vestonice does. Considering that Villabruna can be modeled as having a small ANE contribution and considering that EHG is modeled to be part WHG I'd say that is normal. That doesn't mean Villabruna is linked to Siberia. See the differences between EHG and Karatiana, both roughly half ANE:

epoch2013, Villabruna cluster and Vestonice cluster are both WHG, but they different. I wrote "Villabruna cluster ... has ANE-like participants (EHG?).", "Vestonice cluster ... has no ANE"-participants, in their formation.

the green dot mammoth clade looks like it might have been separated from the rest by some kind of mammoth barrier around the Urals which then disappeared around the 14-24K mark allowing mammoth clades from the east to move west.

i was originally thinking that would make a very convenient r1a/r1b split but apparently the dating doesn't fit but as a time for R1 generally to follow herds west maybe?

if the R1b/R1a split was some geographical barrier further east and R1b were on the western edge of it they might show up first?

My mtDNA database keeps growing and now I have enough mitogenomes to show irrefutable of recent Steppe mtDNA in Iran. Several pan-European U4 and U5 clades show expansions around 5,000 years ago and several of them are also found in Iran. All of them have been found in LNBA Europe.

I don't know how accurate this is but there is a theory about the Volga River and Caspian Sea being absolutely huge covering the whole Khvalynsk Basin and almost reaching as far North as the Urals when the Glaciers started to melt. Maybe this created the substantial barrier before and after the LGM ?

Just to be sure: Most of us use the abbrevation "WHG" for Loschbour because Lazaridis used it in his paper. De abbrevation obviously means "Western Hunter-Gatherer", which would certainly include Gravettiab, but I think it is used as a synonym for the Villabruna cluster, which excludes Gravettian.

@MaxT, thing is neither Fu's nor Reich/Lipson's models actually resolve relationships between ancient UP Euro related HGs (inc. MA1 and AG3) at the same time as resolving relatedness between them and East Eurasians.

Ancestry from a population which is an outgroup to the main UP EuroHG clade could well be making MA1 look like more like an outgroup to the UP EuroHG clade, if it's quite significant, and if there's very little shared drift with MA1's ancestry as a member of the UP EuroHG clade (and it would have to be very little).

@Rob, not confident enough in my knowledge of the Upper Paleolithic European samples to answer. More adna is always better. Tianyuan Man's sample will maybe shed more light on what is happening with differential relatedness to East Eurasians, which is a major question here (since it is at the root of where MA-1 and Villabruna cluster members fit with other UP Euro-Siberians).

Semi on topic ramble, when motivated to go back to Fu et al, I had a look over their qpWave analysis again. qpWave is something I've sort of ignored before as telling us what we already know. The function is use f statistics on a two sets of "left" populations and "right" populations, to get an N of how many sources are needed for differential relatedness in "left" pops to "right" pops.

("The papers that introduced qpWave showed that if the Left populations are mixtures – in various proportions – of N sources differently related to the Right populations, then all f4- statistics of the form of Equation S13.1 will be consistent with being a linear combination of N vectors of statistics that correspond to the mixing populations, and the matrix will have rank N-11,2. We can test whether this is the case using a Hotelling’s T test").

Anyway, in the case of the Villabruna cluster, this produces "Rank 2 is consistent with the data (P=0.41). This again supports the model of few as three ancestral populations, although the truth could of course be more."

"The qpWave analysis is able to document that at least three sources are necessary to account for the allele frequency correlation patterns in Villabruna Cluster samples. However, we did not succeed at convincingly modeling the ancient relationships among these sources."

They go on to suggest that they were unable to totally model these sources, however, they suggest 1) a "common thread" (main ancestry), 2) a source for "variability in the degree of allele sharing with ElMiron/GoyetQ116-1" and 3) finally, a source which relates to the variability in sharing with East Eurasians (it is important to note that V cluster is not homogenous on this, nor does this simply covary with sharing to Magdalenian / Aurignancian).

Apparently, they do not interpret that separate sources are required for relatedness to Near East or MA-1 itself, within the VB cluster, to the limits of their resolution (which we could consider more extensively now with the greater numbers of Euro Mesolithic HG samples published in 2017, e.g. Iron Gates, Latvian, etc. and to note they do just use WHG proper and not include Motala_HG, Karelia_HG, etc.).

So perhaps the question for V cluster is these three sources really, and where they fit on a tree. Then understanding how this integrates with the archaeology of the Epigravettian...?

On that, wonder if the labs are using qpWave in this way - first identify sets of subclusters, then run qpWave on each cluster to understand the minimal set of sources each cluster breaks down into, then try and fit them all on onto a qpGraph, with the constraint that members of each cluster should have the number of sources on the qpGraph as required by qpWave.

It's beyond theory; geology doesn't allow any doubts about the early Khvalynean basin filling up and overflowing into the Black Sea for a while post-LGM.

And while the overflowing Caspian and (no to be ignored) Aral basins, and the spillways these created, did form barriers, I think one must consider that this not that dry Central Asia also provided a more hospitable environment for both HGs and perhaps also early pastoralists than what you find there today.

Yes I agree. Central Asia could have looked much different.However how did the Khvalynsk Basin look like Pre-LGM ? Was this not also a warmer period with some melting maybe not as extensive as Post-LGM but enough to maybe create huge marshes which most animals avoid travelling through ?

"The Khvalynian-era Caspian Sea separated the western steppes–thosewest of the Ural Mountains–from the eastern steppes of Kazakhstan and CentralAsia for about 2000 years, from 16,000 to 14,000 BP. East-west travel on footwas possible only across the Ural Mountains to the north. Earlier, during the coldLast Glacial Maximum, the Upper Paleolithic cultures of the Siberian steppeseast of the Ural Mountains already were somewhat different from those west ofthe Urals (Boriskovsky 1993; Lisitsyn 1996), but during the Khvalynianflooding, the expanded sea cut off contact, isolating the cultures of the westernsteppes even more from those of Kazakhstan and Central Asia. As a result, thedifferences between them intensified. At the end of the Pleistocene, the spreadof forests across the former mammoth steppe created an ecological contrastbetween the southern steppe cultures, which continued to hunt wild equids on theopen plains, and the cultures of the north, which slowly adapted to life as forest-zone foragers.After the Caspian retreated to approximately its modern basin (afterabout 12,000 BP), the landewly exposed by the K hvalynian regression, theNorth Caspian Depression, became a dry and challenging environment (Figure1). A large sand desert called the Ryn Peski, or Red Sands (now the northern-most sand desert in the world), lies north of the Caspian and northeast of theVolga delta. "

There seems to have been no "South Ural refuge" either, there are like 3 sites there during the LUP, but maybe supernord knows something new ?

Thanks. I guess we really need some samples from between 30 & 15 ky BP from east of Europe.

The EPiGRavettian network did stretch from Iberia to the Caucasus, so it could be a mediator of transmissions. As I 've said earlier in the thread, the Siberia route seems to come into play fairly late on - ~ 11 000 YBP arriving in Volga region with microblade techniques.Until then west of the Ural region was repopulated from the west - southern aspect of the Russian plain, and some notable movements from the Caucasus to Stavropol region.

Its interesting the La Brana has that Eat Asian affinity, being so far southwest, whilst Villabruna lacks it. How did Han affinity vary with affinity to MA-1 ?

He was in favor of the Armenian Highlands - Lake Urmia region, according to some biography I have just found on the internet.

Ric HermThere is an article about Caspian and Black Sea sediments that I liked. Good starting point if you want to dig into the details, because in contains a lot of references. http://www.sciencedirect.com/science/article/pii/S027737911630227X

It says that the level of the Caspian Sea was probably higher than now in the entire 50 000 ya (give or take) to end of Pleistocene period. They show that in the 19 000 ya - 13 800 ya period there was a considerable glacial meltwater inflow to the Caspian. It stopped around 13 800 ya, because the ice retreated outside of the Volga catchment area. They could not say anything for sure about before 19 kya, because their sediment samples were not old enough for that.

Before 19 ky BP, at the peak LGM, whatever rivers would have been frozen over and Caspian-Aral seas very low, making crossing across it possible, we can presume.But this was definitely cut off after the LGM, until fairly late. The Mesolithic groups which re-colonized the north Caspian region show no links to Siberian foragers across the Urals.

"It is a mistake, because no Mesolithic groups from the north Caspian region were tested! Samara EHG has link to Siberian Mal'ta/Afontova Gora men.'

It's funny how confident you are with yourself, given that you often fail to grasp the nuanced details.

The early Mesolithic "After the Caspian retreated to approximately its modern basin (afterabout 12,000 BP), the lannde wly exposed by the K hvalynian regression, theNorth Caspian Depression, became a dry and challenging environment (Figure1). A large sand desert called the Ryn Peski, or Red Sands (now the northernmostsand desert in the world), lies north of the Caspian and northeast of theVolga delta. During humid periods, the Ryn Peski was covered by steppe, andin dry periods, as today, it reverted to desert. The Caspian Depression elsewherehad a floor of variegated clay anndd sya soils, dotted with brackish lakes andcovered by dry steppe containing salt-tolerant stands of Artemisia. Occasionally,winds exposed fossil shoals of oDldre issena shells. Herds of saiga antelope(Saiga tatarica), onagers E(quus hemionus ), and horses (Equus caballus) werehunted across these saline plains by small bands of post-glacial hunters. Theircamps have been found among the dunes northeast of the Volga at places suchas the Early Mesolithic site of Je-Kalgan (Dzhe-Kalgan) and the Late Mesolithicsite of Suek-Te. Similar flint tool kits, containing geometric microliths in lunateand trapezoidal shapes as well as end-scrsa poenr small blades, were used in sitessouth of the Volga, as at Kharba. Igor Vasiliev (Vasiliev et al. 1996; Vasiliev1998) has compared these tool traditions to those of the North Caucasus (atMesolithic sites such as Satanai and Tomuxlovka) and has suggested that theCaspian steppes were re-occupied after the Khvalynian flood by forager groupsfrom the south. It is probably unwise to rely solely on lithic tool kits to identifythe ethnic and geographic origins of forager societies, but on the strength of theevidence, similar microlithic tool kits were used during the Mesolithic over alarge region that included both the Caspian Depression and the North Caucasus."

by contrast "Earlier, during the cold Last Glacial Maximum, the Upper Paleolithic cultures of the Siberian steppes east of the Ural Mountains already were somewhat different from those west of the Urals (Boriskovsky 1993; Lisitsyn 1996), but during the Khvalynianflooding, the expanded sea cut off contact, isolating the cultures of the westernsteppes even more from those of Kazakhstan and Central Asia. As a result, thedifferences between them intensified." & again "In contrast, Mesolithic foragers living east of the Caspian Sea and east of the Urals made quite different kinds of tools andseem to have belonged to distinct social networks"

'Samara EHG', dates to 5500 BC, which is Late Mesolithic, making it some 3, 500 years after the appearance of Afantov-Gora microblade industries in northeastern Europe, which accounts for the ANE admixture seen in 'EHG".

@Rob, your categorically allegations are unreasonable ("The Mesolithic groups which re-colonized the north Caspian region show no links to Siberian foragers across the Urals."). You just wrote Mesolithic, but not early Mesolithic. No genetic data on early (and too late) Mesolithic of the Northern Caspian Sea, the Urals, Siberia is present, therefore your assertions are unfounded. Any personal opinions not related to the distribution of people don't have weight. Just do not understand archaeology may think that the archaeological assumptions have in this issue big weight.I wrote you that your declaration that "groups" "show" "no links" is mistaken. They may have a southern connections, but it does not means that they don't have еastern connections. Nobody knows.

by contrast "Earlier, during the cold Last Glacial Maximum, the Upper Paleolithic cultures of the Siberian steppes east of the Ural Mountains already were somewhat different from those west of the Urals (Boriskovsky 1993; Lisitsyn 1996), but during the Khvalynianflooding, the expanded sea cut off contact, isolating the cultures of the westernsteppes even more from those of Kazakhstan and Central Asia. As a result, thedifferences between them intensified."

Early Kvalynsk transgression 17000-10500 BP had been interrupted Eltonsk regression. Phases of transgression and regression of the Caspian sea were changed constantly every few thousand years. But even it doesn't mean anything because people still could pass freely in any time, no physical barriers for this was not. The Eppigravettian culture of Moldova started approximately 20000 BP.

@ Samuel Andrews. Came across this in my research on MtDNA H6.”MtDNA H6a was involved in a late Upper Paleolithic expansion from the southern Caucasus or Near East.” Is there a possibility that H6a lived in the Zagros Zarzian Culture? Eupedia.com includes H6a in Mesolithic Ukrainian MtDNA.

Are there any similarities to Upper Paleolithic Eastern Siberian & Native American lithic reduction techniques? Behind my house, in the woods, there is an chert quarry that the Archaic Native Americans utilized. ( the chert is super chalky and was “cooked” in Earth ovens. I have found 3 Earth ovens in the woods) The chert cores left by these Native Americans resembles a long rectangular core with 4 distinct sides. I was wondering if this lithic reduction technique was used in Upper Paleolithic Eastern Siberian sites.

Om anthrogenica some one connected the Kapova Cave to ANE or EHG survival during LGM. We know that EHG is roughly half ANE and half Villabruna. I have a hard time finding anything on Kapova cavem but we know (Epi-)Gravettian in Moldova came from the west IIRC.

You need to stop obfuscating, because it severely undermines your relevance. And try not using words which you don.t understand the meaning of.

My ´´allegations´ are sourced materials from relevant specialists. I know what samples we have and don't have, the entire point of the discussion was hypothesizing based on archaeology. IF we had aDNA, we wouldnt be having the debate. So, no need for irrelvant side-points.

'But even it doesn't mean anything because people still could pass freely in any time, no physical barriers for this was not.'

Yes i did note that point above!. But the archaeological picture is nevertheless one of increasing divergence between the tehcnocomplexes on either side of the Urals.

So here it is again '"Earlier, during the cold Last Glacial Maximum, the Upper Paleolithic cultures of the Siberian steppes east of the Ural Mountains already were somewhat different from those west of the Urals (Boriskovsky 1993; Lisitsyn 1996), but during the Khvalynianflooding, the expanded sea cut off contact, isolating the cultures of the westernsteppes even more from those of Kazakhstan and Central Asia. As a result, thedifferences between them intensified." & again "In contrast, Mesolithic foragers living east of the Caspian Sea and east of the Urals made quite different kinds of tools andseem to have belonged to distinct social networks"

I presented literature, if you want to be taken seriously, do the same.

Here's more ´´The Trans-Urals and apparently even the north Siberian Arctic remained ice-free even during the LGM (Astakhov, 1992) and except for water-saturated and frozen boggy lands (Fig. 19) there were no major natural obstacles for movement of Palaeolithic groups further east into NW Siberia prior and after that time interval´´ http://www.sciencedirect.com/science/article/pii/S104061820900278X

Again, I note that diretion must have been bidirectional, but the main Afantova impact came the Terminal Palaeolithic.

If you have literature showing something else or new - please share it.

'The Eppigravettian culture of Moldova started approximately 20000 BP.´Yes, and ?

@epoch2013, In the LGM age in the Urals and behind it were boreal forests such as in the Balkans and in the South of Spain. Behind the Urals at that time was not of the glacier in contrast to Europe. In contrast to Western and Central Europe where there were glaciers and tundra, there was widespread steppe. Sungiric so generally lived near the glacier.

@Rob, I think you do not understand the texts referenced, confusing times and it is not clear that, so the answer something impossible.

@jv,"Is there a possibility that H6a lived in the Zagros Zarzian Culture? Eupedia.com includes H6a in Mesolithic Ukrainian MtDNA"

No H6a was found in Ukraine Mesolithic, I don't know why Eupedia claims so. I guess it's possible H6a lived in Zagros Zarzian culture. There's really no way to tell. My opinon on H6 han't changed. I've gotten more European mitogenomes and it keeps telling the same story: H6 in Europe is uniform and is the result of a "recent" expansion from the same source (Steppe).

"I'm not sure what you are trying to say with the tethered thing. If your ecological niche covers a wide area why would you be stuck to one corner of it?"

Which is why, IMO, ANE probably first came via the boreal zone of Eastern Europe- the middleVolga region. It's quite easy to trace: microblades develop in TransBaikalia 20-18ky BP, a new, slightly different population (AG-like vs MA-1 like) with a distinctive material culture re-emerges from the refuge, reaches western Siberia by 16-14 ky BP, and then onto Eastern Europe after a couple G years delay.

They have nothing to do with EpiGravettian mammoth hunters with mammoth bone houses, which is an extinct culture

The Iberian refugee had Solutrean culture, distinct from the Epigravetian.I guess a barrier of sort prevented cultural and also genetical influence between the two refugees during the LGM.

What would you think about a group of ANEs, living an Eskimo-like way on the sea edge of the glacier and spreading over it up to Iberia, bring the East Asian affinity, the Clovis-like blades, and maybe also R1b to there?

Right on - VB, and its haplogroups, could not come from Siberian Afantova Gora like groups.But it could come from the meta-population which migrated to south Europe, Siberia , & Near East b/w 35 & 25 kya .

What would you think about a group of ANEs, living an Eskimo-like way on the sea edge of the glacier and spreading over it up to Iberia, bring the East Asian affinity, the Clovis-like blades, and maybe also R1b to there?

In the context of Rob's comment ("Its interesting the La Brana has that East Asian affinity, being so far southwest, whilst Villabruna lacks it"), there's not so much sign of higher ANE in La Brana relative to VB though, is a drawback.

I was toying with the idea that, patterns in VB cluster could be explained by:

On the negative about that is that Mathieson's 2017 qpAdm puts about 16% EHG (8-10% ANE?) into Koros_HG (Hungarian KO1), only (https://imgur.com/7at24HX / https://imgur.com/mFjBBT1), and that is in theory seems like it would be the most extreme population on the WHG->EHG cline - https://imgur.com/M4TkAmV (from Lipson 2017) of those surveyed by Fu et al 2016.

LOL. When you describe it like that, it does sound crazy. But hear me out: The RUssian plain mammoth hunters which c. 16 kyBP could have arrived from further west, Moldova and even Moravia, Lower Austria, etc, literally chasing the last of the mammoths, east. So it could be that the Siberian hunters were potentially distinct, although Of course they'd have some kind of contact. Interestingly, the faunal assemblages in Siberia during the Late Palaeolithic were dominated by reindeer, Siberian mountain goat, bison, red deer, etc. Only few sites had mammoths, like Afantova Gora.

@ RicStill need more aDNA, but there were probably a chain of movements in Late Palaeolithic, and there'd be multiple vectors for spread of specific lineages. Maybe R1 was near the east Casian during the LGM ?

The idea that R1 came from LGM Central Asia was forced by some assumptions that have been proved erroneous by ancient DNA. For instance, that R1a was native to South Asia and that R1b-V88 was native to the Near East.

We now know that these lineages are native to Europe, so R1 could well be native to Europe as well, having arrived from Siberia as pre-R1 in Eastern Europe sparsely populated by Kostenki/Sunghir-related groups.

@ Dave No, I was not basing my guess on studies from 2004, if your reply was in regard to that. More to the possibility of now a rich biomass zones whose sites were destroyed by sea level changes, etcBut sure a pre-R1 scenario makes sense

@David - "We now know that these lineages are native to Europe, so R1 could well be native to Europe as well, having arrived from Siberia as pre-R1 in Eastern Europe sparsely populated by Kostenki/Sunghir-related groups."

I think it would be a bit academic to call it pre-R1 versus R1* since it'd just be a question of what SNPs are used to define R1 going forward if we find ancient offshoots from this branch.

@Rob - I think big game hunters can be pretty mobile still. Take the indigenous peoples of the Great Plains in North America for example. I don't see why their relatives on the Eurasian steppe would be very different.

Yes Alaskan Caribou travel as much as 5000 kms during their migration and some African desert elephants migrate up to 500 kms.

So huge distances could have been covered by Hunter Gatherers if they followed the Herds and it is not difficult to imagine that herds would have shifted their migration path if conditions gradually deteriorated in their original range.

I have no doubt they were mobile and chased game around. I'm just pointing out that the only thing we appear to see in Western Russia at this point (25-16ky BP), is migration from the west and south. So instead of carrying on like a broken record about game hunters, why don't we reflect on what the evidence is actually showing ?

@ RicOkay. Maybe you can scrounge around for some eastern / Siberian industries appearing c. 20'kya , because that would fit the bill for R1.Because I'm not doubting the possibility, even likelihood, but I can't recall ever reading about such a phenomenon.

I think a lot of things happended near the Altai Mountains. I see a possibility of Haplogroup R forming somewhere between Ust Ishim and the Carpathians.

If K2a* could be in that area I can not see why K2b* and their later relatives could not have been there to. We see Denisovans, Neanderthal and Modern Humans all in the Central Asian Altai melting pot.

We know that Neanderthals which contributed to the Modern Population were of West Eurasian stock so there had to be a migration from the Carpathians/Crimea/Urals or the Caucasus/Zagros to where Ust Ishim Man eventually ended up. I think the Neanderthal admixture could be a clue from where the ancestors of Mal'ta Buret originated from. So those women figurines could still be connected to Europe after all....

@Ric - "We know that Neanderthals which contributed to the Modern Population were of West Eurasian stock so there had to be a migration from the Carpathians/Crimea/Urals or the Caucasus/Zagros to where Ust Ishim Man eventually ended up." Huh?

Ryan" I think big game hunters can be pretty mobile still. Take the indigenous peoples of the Great Plains in North America for example. I don't see why their relatives on the Eurasian steppe would be very different."

sure but limited by the extent of the biome. if hunters followed herds of x they'll remain within the bounds of the biome that supports x.

(seems to me the idea of bands following herds 1000s of mile might explain how a more or less homogeneous population could be maintained over a huge area i.e. if different bands swapped brides when they bumped into each other on their travels.)

We really need Adna from Southeast and/or East Asia etc. it's already proven that modern diversity and frequencies can be misleading about it's origin and expansion like the R1a situation in India/Iran.

1. I pretty sure nobody here arguing for _all_ West Eurasians migrating from SE Asia. There is an argument for an ancient migration that had significant impact on male lineages, but even that is only for branches under K. I am yet to see any argument for G, I, J or E coming from SE Asia. And the genome-wide impact of K branches is not necessarily as big as the Y-DNA impact.

2. The assumed SE Asian source population for the K lineages being Denisovan admixed is not self evident at all. Most East Asian have a lot smaller Denisovan ancestry than Neanderthal one and populations from the most likely source area, continental S-SE Asia, are not very well studied from this angle, as far as I know. So how did they dodge Denisovan admixture? The answer is that we do not have any information whether there was anything to dodge.

So if I am not totally confused this tells me that Haplogroup K originated somewhere else than Southeast Asia and split into different migrations....? Maybe rather from the Caucasus or the Zagros Mountains...

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>DNA and isotope analyses on human skeletal remains are an effective tool to explore human mobility in the past. This mobility, in turn, formed the basis for the exchange of objects, knowledge and practices. A special emphasis of this project is on the investigation of bacterial DNA. Pathogens and human mobility in prehistoric times developed a significant dynamism, which could transform entire habitats and culminate in extensive movements of populations. From the intersection of isotope, DNA and pathogen analyses, with a well-founded historical and archaeological background, the researchers will be able to draw a dynamic picture of the past.

>At the core of MHAAM are three research areas:

>1. The first "globalization" of the eastern Mediterranean area in the late Bronze Age and early Iron Age (ca. 1600-1000 BC).>2. The so-called "Phoenician" and "Greek" migrations in the early 1st millennium BC throughout the Mediterranean.>3. The link between human mobility and the spread of diseases in ancient times.

Why the Caucasus or the Zagros mountains? Why not Afghanistan, or Pakistan, or Mezopotamia, or India, etc.? What is the difference? This is just random guessing at this point. I could say India is a better candidate, because of its central position between IJ and K and also H is pretty India specific. But with the time passed since then this might mean nothing.

Also I still do not understand what is your problem with Denisovan admixture. - We do not know where the Denosovans lived.- We do not know where the Denisovan mixture happened and when. - We do not know what later migrations carried around or diluted the Denisovan ancestry, and where and when.- We do not know if there was any Denisovan ancestry in the part of SE Asia where and when the supposed P (or P precursor) population might have lived. (And the fact that we do not know where and when this population lived is not helping either...)

With this many "we do not know" the Denisovan ancestry vs. P ancestry is pretty much just a phantom, not a real problem.

That being said, Denisovan admixture isn't ubiquitous in SE Asia. The Onge seem to have managed to dodge it. Keep in mind that the indigenous populations in the Americas with the most Denisovan admixture have the least Oceanian admixture too. If that Oceanian ancestry came from ANE, then it lacking Denisovan admixture is exactly what we would expect.

The Neanderthals responsible for most of our Neanderthal ancestry probably just haven't been sampled yet, so I wouldn't read too much into which fringe population of Neanderthals is closest to us when all we have are samples from fringe populations.

If memory serves though, prior to the recent sequencing of this Croatian Neanderthal, Altai Neanderthals were the best match for the Neanderthal ancestry in all Eurasians, but Iberian Neanderthals were the best match for the Neanderthal ancestry specific to East Asians. So at the very least Neanderthal population structure wasn't very intuitive.

"Why the Caucasus or the Zagros mountains? Why not Afghanistan, or Pakistan, or Mezopotamia, or India, etc.? What is the difference?"

We may not have any good idea on where Denisovan lived. But we have a very good idea where Neanderthals lived. And *all* Eurasians have a considerable Neanderthal admixture proven to be from non-Altaic Neanderthals, and dated to 55k ya.

The Caucasus and Zagros mountains are inside known Neanderthal area, the rest isn't.

44:35 - Map of the spread of steppe ancestry and Beakers. I don't know how meaningful (or -less) this is, but "Yamnaya pastoralists arrive from the steppe ~5,000 ya" arrow points from Ukraine to the North-Western direction.

56:20 - Isotopic analysis of Beakers from Britain shows that less than 0.5% of people had non-local signature. Yet DNA shows a massive migration. How it's possible? Strontium isotope signature from the Netherlands and Northern France is virtually indistinguishable from the British one.

50:30 - Temporal data allow to better understand the dynamics of population change and they are moving in this direction. E.g. they have now a time-series of data from Hungary that shows continuous HG admixture in farmers.

"But we have a very good idea where Neanderthals lived. And *all* Eurasians have a considerable Neanderthal admixture proven to be from non-Altaic Neanderthals, and dated to 55k ya."

We actually do have strong constraints on when and where most Denisovan admixture occurred. We know that eastern Neanderthals, but not western ones, had Denisovan admixture. And we know that the ancestors of the people who crossed the Wallace line had to have picked up their Denisovan component after the shared '55k ya' Neanderthal event in the west, but before crossing the water in the southeast about 50k ya.

We also know that some African-like 'modern humans' and some very divergent (erectus?) were around Asia at some time within the last 200,000 years, but before the major Out of Africa event.

And where were all the Basal Eurasian populations for so many years? I suspect in North Africa, away from Neanderthal contact, and only arrived in Eurasia in somewhat later OOA events that couldn't get past the fertile crescent without admixing with the locals hunter gatherers they encountered.

Denisova > MA1 flow may be an issue of using Altai instead of Vindija as the Neandertal. Altai has AMH admixture, so a bit of deeper archaic may be asked for. When I use Vi_merge, or combine Altai and Vi_merge, there is no Z >2 asking for Denisova ancestry in MA1.

Minimal presence of the main Amerindian component (RED) in one of the Sunghir individuals at 34,000 (https://genetiker.wordpress.com/). Tianyuan (40,000) has more. Kostenki even more. Yuzhnyi Olenij Ostrov (karelia) (7000), Okunev, Khvalynsk, etc. even more. Mal'ta has the most.

A secondary Amerindian (or Beringian) component (ORANGE, peaks in Eskimos and Paleosiberians) is also found in Sunghir individuals, and it's more pronounced than the main Amerindian component.

Re: the talk and Bronze Age Beaker Brits, not really much change at all in the broad picture (almost total replacement), but Reich's talk did show expanded sampling compared to Olalde's original preprint, and there are a few details from their extended panel of sampling:

https://imgur.com/a/f1kZZ

Series of images contrasting preprint with newer data.

Looks like this firms up complete replacement in early samples, with some "choppy" admixture, then a low level of Britain Neolithic in the later samples. But it is a very low level - 10% ish. (Could even reflect just more migration from Bell Beaker groups in e.g. France).

Of course, this is basically the same as preprint, but higher sample size firms up the trend.

Thank you for the link! However, the male migration from the Steppe WAS NOT entirely male! MtDNA H6a1a and other “new” to Central & Northern Europe MtDNA lineages were introduced during these migrations.

@Grey - that seems to show mammoths as migrating across Eurasia just fine. Keep in mind too that minor geographic barriers can create a fair amount of structure in populations. Take elephants for example - the European elephants that went extinct in Europe ~30,000 years ago were more closely related to African forest elephants are to African bush elephants. Their mtDNA actually falls within modern African forest elephant's mtDNA variation. That doesn't mean that it's harder for an elephant to walk from the savanna to the adjoining forest or visa versa than it is for a forest elephant to migrate all the way to Europe. It just means forest elephants happened to be the ones that made that migration.

It does not really effect your argument, but those European elephants were probably hybrids. It is just that the Asian elephant admixture was male mediated. Of course this still mean that some African forest elephants had to make that migration.

@Ryan"that seems to show mammoths as migrating across Eurasia just fine"

sure, at a later date - hence the possibility of there being barriers which later disappeared and specific clades going extinct behind a barrier but that space getting refilled later with different mammoth from beyond the barrier.

Assuming all I2 from Britain Neolithic, suggests slight sex bias with MBA having potentially 13% Britain Neolithic female ancestry and 8.9% male, which averages out at 10.8% autosome. But it's not really looking sex biased, mostly just low for both, esp. if we assume a bit more noise on the y (sample size only 11 and uniparentals are generally noisier).

....

Interesting to compare to Spain, which has survival of Iberian CA that is roughly 2.5-3.5 times higher (looks about 25%-35% SpainCA).

In Spain it looks like there is that early wave who have low steppe ancestry, followed by a general increase and also likely admixture from a eastern / southeastern vector.

Perhaps in Iberia, there was a difference that the first wave of migrants from the northern Beaker complex assimilated into a more shared culture which had already received cultural influence from them (e.g. used the same beaker pottery?), and then adopted proto-Basque Iberian speech and mythology?

Later on there was then another "top up" of steppe ancestry from Celtic migrations in the late Bronze Age?

While in Britain, only one wave with some low survival of British Neolithic people. Perhaps with a few ideas along the way - Razib Khan speculated that cthonic and fertility gods of NW European mythologies (Germanic, Insular Celtic) may derive from cultural transmission from Middle Neolithic farming peoples (though this is a really speculative) - and maybe some continued use of some of the British Neolithic sacral sites (the henge temples, the temple complex at Skara Brae, etc.)...

The Y frequencies are not as granular as the autosome, so using these small comparisons to estimate sex bias is actually meaningless. Most likely there was just no sex bias in this particular situation.

@Matt - "The Y frequencies are not as granular as the autosome, so using these small comparisons to estimate sex bias is actually meaningless. Most likely there was just no sex bias in this particular situation."

You can use the X-chromosome, which Mathieson did, and found a HUGE sex bias.

If someone eventually looked at it, there could be a X bias in absence of any lower Y than autosome, somehow. It doesn't seem very likely though!

I still have questions about whether that method really works though. I'd rather see it demonstrated through simple f4 ratios and stat comparisons on X and autosome a la Charlston Chiang's paper on Sardinia, prior to these complicated qpAdm methods.

Can't discuss lineages with you guys. One thing caught my attention though. 'Following the herds for 1000s of miles' is not within the realm of probability. That would be a really strenuous and one-sided existance. There's other things to do apart from running. Herds travel fast!Hunter-gatherers have quite a full agenda along a range that is unlikely to supersede 100 miles. Crossing the trail of herds is important, but so is keeping in touch with the grapevine (mating!), attending the fruittrees and honeycombs and salmon-runs, etc etc. Losing touch with the smoke of the camps of your kin, and finding the tryst-places void of messages spells mortal danger for your group!That said, cultures may spread very long distances within five or six generations when the numbers are swelling, and the lands are empty of 'others'. And to us that looks like the blink of an eye.There is always Murphy's Law, and those that have survived knew how to circumvent adversity. I often speculate about the shaman's role here: paleological consciousness is so far apart from ours. But it was obvious to me from the start there was something fishy about the Clovis-hypothesis. This was hardly a theory of well-meaning scientists, but obviously pushed by people with a very different agenda.Let's face it: no group is gonna make it from Beringia to Vuelta del Fuego in 1000 years! They would have had to borrow motorcycles from the future to race down (non-existant) sandy beaches, all the while muttering: 'Can't keep Dillehay waiting, now can we?' Boats then! They could have made it in boats! Ah me! How many? Motivated by what? Why not stop off in sunny California and sprawl in the sun?South America is much much older than the LGM, but North American academia simply wouldn't have it. Budgeting, I presume.Academia has laws of its own, and they're unwritten, but understood by all that want a career in this field. Our David here understands that better than most. But he's also committed to the 'truth' (whatever that is!?). There are more agendas out there: crackpots who want to unmask crackpottery, hobby-horse riders, identity-(re-?)searchers, the Indo-Europeans (Indo versus European, so basically us-and -them guys), and searchers. By that last I refer to people for whom many things are still up in the air. They have a stake but are unsure about it. The searchers are all nice guys! There's also the observers, like me. They have no stake. They're probably cowards, looking for a bit of action when it is cheap. They won't be there when payment is required. So here I am now with my finger on the post-button. Have I said anything meaningful in this post? Going from distance-covering to academia? Structure of a child's essay ... Well, what the heck ...

Note: the claim about mammoth kill site in Northen Siberia 45 000 years ago was disputed at another paper:

http://www.sciencedirect.com/science/article/pii/S1040618216302105

" The few minor traces of carnivore scavenging, the little disturbed condition of the carcass, and the absence of bone modifications made by human actions, along with the social status of this young male animal, are interpreted here as highly probable evidence that the Zhenya Mammoth died from unrecoverable injuries inflicted during a bull-to-bull fight."

Speculation : However I can see how some human interaction could have been present without leaving a significant trace.

Eg. A small band of hunters encountering two fighting bulls or an injured bull which could have triggered their opportunistic instinct. All they maybe needed to do was cut the trunk artery to secure their prize. They could have been on the hunt for something else and didn't expect or prepare for this scenario and could have cut only a few choice pieces of meat because of a significant gathering of carnivores.....

@Matt - Yah, I'm just saying it could be done. And it'd be nice to do both approaches to compare them.

@Chad - "Denisova > MA1 flow may be an issue of using Altai instead of Vindija as the Neandertal. Altai has AMH admixture, so a bit of deeper archaic may be asked for. When I use Vi_merge, or combine Altai and Vi_merge, there is no Z >2 asking for Denisova ancestry in MA1."

Vindija's DNA has only be out for a week though hasn't it. If you've done any analyses using her DNA I'd be curious if anything interesting jumped out at you.

>epoch2013, if you go by the model Ancient North Eurasians being Sunghir+ENA (which seems worth testing eventually in qpGraph, though seems hard to know how anyone can know without testing), then it may not be a single small population and it may just be than all these populations are varying independent mixes of the Basal_Eurasian+Villabruna+Sunghir+ENA ancestries. I am not sure about this though.

While ANE was of course admixed it seems to have a different type of West Eurasian ancestry than the Vestonice Cluster, and the Villabruna Cluster did. So they must have had split very early. Pre-Kostenki14 is a good bet. Due to Bronze Age invasions Modern Europeans seem to have more of that ANE-type West Eurasian admixture than Villabruna/Vestonice types of ancestry. It's indeed possible Paleolithic Europeans were admixed with other Eurasians, but it's also could be that all of these paleolithic pre-LGM Eurasians shared a significant part of their alleles because their divergence dates weren't that distant, yet.That may be the reason why ADMIXTURE results for UP Europeans are so mixed, yet QpGraph suggests they in fact weren't admixed with other populations.(Though Sunghir is supposed to be admixed with Proto-WHG)However gpGraph can create many different models so it's impossible to tell without Paleolithic and Mesolithic samples from East Asia, South Asia/Oceania, and West Asia, along with pure Paleolithic and Mesolithic Basal Eurasian samples. It's possible all Paleolithic Eurasians were initially Ust'-Ishim/Oase/ASI-like.For one, some formal statistic tests do suggest that GoyetQ116-1 was admixed with something closely related to Tianyuan, and Tianyuan is supposed to be the ancestor of mongoloids. So other UP Europeans could also had>epoch2013, if you go by the model Ancient North Eurasians being Sunghir+ENA (which seems worth testing eventually in qpGraph, though seems hard to know how anyone can know without testing), then it may not be a single small population and it may just be than all these populations are varying independent mixes of the Basal_Eurasian+Villabruna+Sunghir+ENA ancestries. I am not sure about this though.

While ANE was of course admixed it seems to have a different type of West Eurasian ancestry than the Vestonice Cluster, and the Villabruna Cluster did. So they must have had split very early. Pre-Kostenki14 is a good bet. Due to Bronze Age invasions Modern Europeans seem to have more of that ANE-type West Eurasian admixture than Villabruna/Vestonice types of ancestry. It's indeed possible Paleolithic Europeans were admixed with other Eurasians, but it's also could be that all of these paleolithic pre-LGM Eurasians shared a significant part of their alleles because their divergence dates weren't that distant, yet.That may be the reason why ADMIXTURE results for UP Europeans are so mixed, yet QpGraph suggests they in fact weren't admixed with other populations.(Though Sunghir is supposed to be admixed with Proto-WHG)However gpGraph can create many different models so it's impossible to tell without Paleolithic and Mesolithic samples from East Asia, South Asia/Oceania, and West Asia, along with pure Paleolithic and Mesolithic Basal Eurasian samples. It's possible all Paleolithic Eurasians were initially Ust'-Ishim/Oase/ASI-like.For one, some formal statistic tests do suggest that GoyetQ116-1 was admixed with something closely related to Tianyuan, and Tianyuan is supposed to be the ancestor of mongoloids. So other UP Europeans could also had been admixed with many different things from other continents to varying extents.